The MS Aquarius, which it charters along with French NGO SOS Mediterranee, had picked up more than 200 migrants, Medical charity Doctors without Borders (MSF) said on Twitter.
Also the bodies of 22 people have been found on a migrant dinghy in the Mediterranean, the aid group has said.
The 21 women and one man were found "in a pool of fuel and water" at the bottom of the boat, off the coast of Libya. They had been on the dinghy "for hours", the aid group said.
Jens Pagotto of MSF told Reuters news agency: "It is still not entirely clear what happened, but they died a horrible death. It is tragic… It seems that water and fuel mixed together and the fumes from this might have been enough for them to lose consciousness."
All the survivors who were on the dinghy, including 50 children, have been transferred to a boat operated by MSF. Most of the people were from West African states such as Nigeria and Guinea. They were being brought to Sicily along with the dead and were due to reach the port of Trapani on Friday.
Another 354 people were picked up by the MY Phoenix, chartered by the Malta-based foundation Migrant Offshore Aid Station (MOAS), the Italian coastguard reported.
More than 3,200 migrants were rescued from the Mediterranean on Tuesday in 25 separate operations. Vessels from the Spanish and Italian navies and other humanitarian organisations were involved.
Thousands of migrants have died or gone missing in the Mediterranean this year, according to figures from the International Organization for Migration.